Multiple sequence alignment - TraesCS7B01G203200

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS7B01G203200 chr7B 100.000 2928 0 0 1 2928 372710064 372712991 0.000000e+00 5408.0
1 TraesCS7B01G203200 chr7B 91.074 829 50 7 2079 2883 240315406 240316234 0.000000e+00 1099.0
2 TraesCS7B01G203200 chr7B 90.380 790 68 3 2083 2871 208962285 208963067 0.000000e+00 1031.0
3 TraesCS7B01G203200 chr7B 97.714 175 4 0 537 711 662001454 662001628 4.740000e-78 302.0
4 TraesCS7B01G203200 chr7B 93.814 194 11 1 528 720 741291892 741292085 1.030000e-74 291.0
5 TraesCS7B01G203200 chr7B 97.872 47 1 0 2881 2927 240317291 240317337 6.730000e-12 82.4
6 TraesCS7B01G203200 chr7A 95.127 1334 44 8 711 2038 425628292 425629610 0.000000e+00 2084.0
7 TraesCS7B01G203200 chr7A 84.400 500 74 3 7 506 425627766 425628261 3.390000e-134 488.0
8 TraesCS7B01G203200 chr7D 95.735 1266 36 7 824 2086 378149965 378151215 0.000000e+00 2023.0
9 TraesCS7B01G203200 chr3D 92.893 802 55 2 2084 2883 397771415 397772216 0.000000e+00 1164.0
10 TraesCS7B01G203200 chr5A 92.991 799 51 3 2086 2883 170087997 170087203 0.000000e+00 1160.0
11 TraesCS7B01G203200 chr5B 93.573 778 49 1 2083 2859 582837727 582838504 0.000000e+00 1158.0
12 TraesCS7B01G203200 chr1D 92.974 797 53 3 2088 2883 430430663 430431457 0.000000e+00 1158.0
13 TraesCS7B01G203200 chr1D 97.872 47 1 0 2881 2927 374481314 374481360 6.730000e-12 82.4
14 TraesCS7B01G203200 chr1D 97.826 46 1 0 2881 2926 458886032 458886077 2.420000e-11 80.5
15 TraesCS7B01G203200 chr5D 93.223 782 50 3 2081 2859 519210256 519209475 0.000000e+00 1147.0
16 TraesCS7B01G203200 chr5D 91.272 802 55 4 2083 2883 557768334 557769121 0.000000e+00 1079.0
17 TraesCS7B01G203200 chr5D 97.872 47 1 0 2881 2927 277617393 277617347 6.730000e-12 82.4
18 TraesCS7B01G203200 chr5D 97.872 47 1 0 2881 2927 557770214 557770260 6.730000e-12 82.4
19 TraesCS7B01G203200 chr2D 94.515 711 36 2 2161 2871 15786379 15787086 0.000000e+00 1094.0
20 TraesCS7B01G203200 chr2D 79.359 562 100 10 1322 1869 533778959 533778400 5.920000e-102 381.0
21 TraesCS7B01G203200 chr2D 88.387 155 17 1 1013 1166 533779103 533778949 4.980000e-43 185.0
22 TraesCS7B01G203200 chr2D 97.872 47 1 0 2881 2927 613220342 613220296 6.730000e-12 82.4
23 TraesCS7B01G203200 chr3A 92.287 752 54 3 2088 2835 726485324 726486075 0.000000e+00 1064.0
24 TraesCS7B01G203200 chr2B 96.316 190 7 0 529 718 184781755 184781944 2.190000e-81 313.0
25 TraesCS7B01G203200 chr6B 95.213 188 9 0 532 719 213152375 213152562 6.130000e-77 298.0
26 TraesCS7B01G203200 chr6B 96.023 176 7 0 537 712 636490820 636490645 1.330000e-73 287.0
27 TraesCS7B01G203200 chr6B 97.872 47 1 0 2881 2927 625388518 625388564 6.730000e-12 82.4
28 TraesCS7B01G203200 chr3B 94.764 191 10 0 527 717 723448621 723448431 6.130000e-77 298.0
29 TraesCS7B01G203200 chr4B 95.652 184 6 2 537 720 300587655 300587474 7.940000e-76 294.0
30 TraesCS7B01G203200 chr4B 94.764 191 6 4 530 720 328009106 328009292 7.940000e-76 294.0
31 TraesCS7B01G203200 chr2A 92.929 198 13 1 518 715 72943272 72943076 1.330000e-73 287.0
32 TraesCS7B01G203200 chr2A 75.467 428 82 15 27 441 407093490 407093073 1.390000e-43 187.0
33 TraesCS7B01G203200 chr2A 75.443 395 77 13 59 441 406965284 406964898 1.080000e-39 174.0
34 TraesCS7B01G203200 chr4A 73.131 428 94 16 12 427 101516880 101516462 1.830000e-27 134.0
35 TraesCS7B01G203200 chr4A 97.872 47 1 0 2881 2927 512016889 512016935 6.730000e-12 82.4
36 TraesCS7B01G203200 chr4D 97.872 47 1 0 2881 2927 439786727 439786681 6.730000e-12 82.4


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7B01G203200 chr7B 372710064 372712991 2927 False 5408.0 5408 100.0000 1 2928 1 chr7B.!!$F2 2927
1 TraesCS7B01G203200 chr7B 208962285 208963067 782 False 1031.0 1031 90.3800 2083 2871 1 chr7B.!!$F1 788
2 TraesCS7B01G203200 chr7B 240315406 240317337 1931 False 590.7 1099 94.4730 2079 2927 2 chr7B.!!$F5 848
3 TraesCS7B01G203200 chr7A 425627766 425629610 1844 False 1286.0 2084 89.7635 7 2038 2 chr7A.!!$F1 2031
4 TraesCS7B01G203200 chr7D 378149965 378151215 1250 False 2023.0 2023 95.7350 824 2086 1 chr7D.!!$F1 1262
5 TraesCS7B01G203200 chr3D 397771415 397772216 801 False 1164.0 1164 92.8930 2084 2883 1 chr3D.!!$F1 799
6 TraesCS7B01G203200 chr5A 170087203 170087997 794 True 1160.0 1160 92.9910 2086 2883 1 chr5A.!!$R1 797
7 TraesCS7B01G203200 chr5B 582837727 582838504 777 False 1158.0 1158 93.5730 2083 2859 1 chr5B.!!$F1 776
8 TraesCS7B01G203200 chr1D 430430663 430431457 794 False 1158.0 1158 92.9740 2088 2883 1 chr1D.!!$F2 795
9 TraesCS7B01G203200 chr5D 519209475 519210256 781 True 1147.0 1147 93.2230 2081 2859 1 chr5D.!!$R2 778
10 TraesCS7B01G203200 chr5D 557768334 557770260 1926 False 580.7 1079 94.5720 2083 2927 2 chr5D.!!$F1 844
11 TraesCS7B01G203200 chr2D 15786379 15787086 707 False 1094.0 1094 94.5150 2161 2871 1 chr2D.!!$F1 710
12 TraesCS7B01G203200 chr2D 533778400 533779103 703 True 283.0 381 83.8730 1013 1869 2 chr2D.!!$R2 856
13 TraesCS7B01G203200 chr3A 726485324 726486075 751 False 1064.0 1064 92.2870 2088 2835 1 chr3A.!!$F1 747

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
981 992 0.104144 TTCCTTGGAGGAACAGGGGA 60.104 55.0 5.33 0.0 46.88 4.81 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2602 2649 0.10741 GGCAACATGACCGGTATGGA 60.107 55.0 7.34 0.0 42.0 3.41 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 4.069232 CGTCCTTGGAGCTCGGCA 62.069 66.667 7.83 0.00 0.00 5.69
32 33 1.078143 GTCCTTGGAGCTCGGCATT 60.078 57.895 7.83 0.00 0.00 3.56
36 37 3.565961 TTGGAGCTCGGCATTGGCA 62.566 57.895 7.83 0.00 43.71 4.92
40 41 1.712977 GAGCTCGGCATTGGCAAGAG 61.713 60.000 11.10 7.92 44.20 2.85
74 75 0.828022 AGTTGGTGTTGGTGTCGAGA 59.172 50.000 0.00 0.00 0.00 4.04
92 93 1.344438 AGACTTCTGTGGCAACGATGA 59.656 47.619 0.00 0.00 42.51 2.92
93 94 1.728971 GACTTCTGTGGCAACGATGAG 59.271 52.381 0.00 0.00 42.51 2.90
94 95 1.081892 CTTCTGTGGCAACGATGAGG 58.918 55.000 0.00 0.00 42.51 3.86
95 96 0.321564 TTCTGTGGCAACGATGAGGG 60.322 55.000 0.00 0.00 42.51 4.30
138 139 1.077993 AGGTAGTCAGCTCTTCCCTGT 59.922 52.381 0.00 0.00 0.00 4.00
139 140 1.903183 GGTAGTCAGCTCTTCCCTGTT 59.097 52.381 0.00 0.00 0.00 3.16
140 141 2.354203 GGTAGTCAGCTCTTCCCTGTTG 60.354 54.545 0.00 0.00 0.00 3.33
149 150 1.421268 TCTTCCCTGTTGTGTCTGCAT 59.579 47.619 0.00 0.00 0.00 3.96
175 176 2.100749 GCCTTAGCTGGTTTGTTGTTGT 59.899 45.455 0.00 0.00 35.50 3.32
177 178 3.380004 CCTTAGCTGGTTTGTTGTTGTGA 59.620 43.478 0.00 0.00 0.00 3.58
191 192 1.330521 GTTGTGAAAGTCGAAGCTGCA 59.669 47.619 1.02 0.00 0.00 4.41
192 193 1.882912 TGTGAAAGTCGAAGCTGCAT 58.117 45.000 1.02 0.00 0.00 3.96
193 194 2.221169 TGTGAAAGTCGAAGCTGCATT 58.779 42.857 1.02 0.00 0.00 3.56
196 197 1.537202 GAAAGTCGAAGCTGCATTGGT 59.463 47.619 1.02 0.00 0.00 3.67
197 198 0.877071 AAGTCGAAGCTGCATTGGTG 59.123 50.000 1.02 0.00 0.00 4.17
205 206 3.188903 TGCATTGGTGGGGTCCCA 61.189 61.111 10.98 7.91 45.02 4.37
229 230 2.278596 CACGATGACGGGCGGTAG 60.279 66.667 0.00 0.00 44.46 3.18
230 231 4.203076 ACGATGACGGGCGGTAGC 62.203 66.667 0.00 0.00 44.46 3.58
236 237 4.388499 ACGGGCGGTAGCTGGTTG 62.388 66.667 0.00 0.00 44.37 3.77
250 251 2.350772 GCTGGTTGGTTCGTTGATCTTG 60.351 50.000 0.00 0.00 0.00 3.02
254 255 3.120786 GGTTGGTTCGTTGATCTTGTACG 60.121 47.826 0.00 0.00 36.67 3.67
255 256 2.679450 TGGTTCGTTGATCTTGTACGG 58.321 47.619 0.00 0.00 36.06 4.02
260 261 0.638746 GTTGATCTTGTACGGCGTCG 59.361 55.000 19.21 8.42 43.02 5.12
286 287 4.382793 GGTGCCTAATTCTCCTTCGTAGTT 60.383 45.833 0.00 0.00 0.00 2.24
289 290 5.044558 GCCTAATTCTCCTTCGTAGTTCTG 58.955 45.833 0.00 0.00 0.00 3.02
306 307 4.742201 GCGTCAGAGCCGGAGCAA 62.742 66.667 5.05 0.00 43.56 3.91
308 309 2.811317 GTCAGAGCCGGAGCAACG 60.811 66.667 5.05 0.00 43.56 4.10
311 312 1.961277 CAGAGCCGGAGCAACGTTT 60.961 57.895 5.05 0.00 43.56 3.60
318 319 0.234884 CGGAGCAACGTTTTCTGGTC 59.765 55.000 0.00 2.99 38.94 4.02
331 332 0.179234 TCTGGTCGCAAGTGGTTGAA 59.821 50.000 0.00 0.00 35.46 2.69
336 337 1.442520 CGCAAGTGGTTGAATGGCG 60.443 57.895 0.00 0.00 35.46 5.69
342 343 0.451783 GTGGTTGAATGGCGTGGATC 59.548 55.000 0.00 0.00 0.00 3.36
345 346 0.802494 GTTGAATGGCGTGGATCGTT 59.198 50.000 0.00 0.00 42.13 3.85
346 347 0.801872 TTGAATGGCGTGGATCGTTG 59.198 50.000 0.00 0.00 42.13 4.10
351 352 0.389296 TGGCGTGGATCGTTGTACAG 60.389 55.000 0.00 0.00 42.13 2.74
381 382 4.422057 TGGTCTCTATAGTGTGGGTTGAA 58.578 43.478 0.00 0.00 0.00 2.69
387 388 3.973206 ATAGTGTGGGTTGAATCGACA 57.027 42.857 2.72 0.00 0.00 4.35
388 389 2.631160 AGTGTGGGTTGAATCGACAA 57.369 45.000 2.72 0.00 0.00 3.18
391 392 2.811431 GTGTGGGTTGAATCGACAATCA 59.189 45.455 2.72 0.00 33.13 2.57
419 420 1.453524 CGAAGTCAGAGTCGTTTGCTG 59.546 52.381 0.00 0.00 32.61 4.41
428 429 4.328440 CAGAGTCGTTTGCTGAGGATTTAG 59.672 45.833 0.00 0.00 0.00 1.85
437 438 3.958147 TGCTGAGGATTTAGGTATGACGA 59.042 43.478 0.00 0.00 0.00 4.20
441 442 6.724893 TGAGGATTTAGGTATGACGATGAA 57.275 37.500 0.00 0.00 0.00 2.57
442 443 6.513180 TGAGGATTTAGGTATGACGATGAAC 58.487 40.000 0.00 0.00 0.00 3.18
444 445 5.602978 AGGATTTAGGTATGACGATGAACCT 59.397 40.000 8.78 8.78 44.47 3.50
447 448 2.906354 AGGTATGACGATGAACCTTGC 58.094 47.619 0.00 0.00 39.32 4.01
448 449 2.236146 AGGTATGACGATGAACCTTGCA 59.764 45.455 0.00 0.00 39.32 4.08
451 452 0.804364 TGACGATGAACCTTGCATGC 59.196 50.000 11.82 11.82 0.00 4.06
457 458 1.985473 TGAACCTTGCATGCTGTCTT 58.015 45.000 20.33 5.12 0.00 3.01
458 459 1.610038 TGAACCTTGCATGCTGTCTTG 59.390 47.619 20.33 4.11 0.00 3.02
460 461 1.214589 CCTTGCATGCTGTCTTGGC 59.785 57.895 20.33 0.00 0.00 4.52
461 462 1.154093 CTTGCATGCTGTCTTGGCG 60.154 57.895 20.33 0.00 0.00 5.69
466 467 0.957395 CATGCTGTCTTGGCGAAGGT 60.957 55.000 8.73 0.00 0.00 3.50
468 469 1.004440 GCTGTCTTGGCGAAGGTCT 60.004 57.895 8.73 0.00 0.00 3.85
473 474 2.357637 TGTCTTGGCGAAGGTCTTTTTG 59.642 45.455 8.73 0.00 0.00 2.44
474 475 1.953686 TCTTGGCGAAGGTCTTTTTGG 59.046 47.619 8.73 0.00 0.00 3.28
481 482 2.290641 CGAAGGTCTTTTTGGAGTGGTG 59.709 50.000 0.00 0.00 0.00 4.17
487 488 1.476085 CTTTTTGGAGTGGTGTGTGCA 59.524 47.619 0.00 0.00 0.00 4.57
489 490 0.254462 TTTGGAGTGGTGTGTGCAGA 59.746 50.000 0.00 0.00 0.00 4.26
515 524 7.992608 AGTATCTTGTATGTGCCATTGTGATAA 59.007 33.333 0.00 0.00 0.00 1.75
516 525 7.828508 ATCTTGTATGTGCCATTGTGATAAT 57.171 32.000 0.00 0.00 0.00 1.28
520 529 9.153721 CTTGTATGTGCCATTGTGATAATTTTT 57.846 29.630 0.00 0.00 0.00 1.94
546 555 8.865590 ATCACGTTTTAATTAACAGTTTTGCT 57.134 26.923 0.00 0.00 0.00 3.91
547 556 9.953697 ATCACGTTTTAATTAACAGTTTTGCTA 57.046 25.926 0.00 0.00 0.00 3.49
548 557 9.440784 TCACGTTTTAATTAACAGTTTTGCTAG 57.559 29.630 0.00 0.00 0.00 3.42
549 558 9.440784 CACGTTTTAATTAACAGTTTTGCTAGA 57.559 29.630 0.00 0.00 0.00 2.43
557 566 8.854614 ATTAACAGTTTTGCTAGAACTCATCT 57.145 30.769 0.00 0.00 42.48 2.90
558 567 9.944376 ATTAACAGTTTTGCTAGAACTCATCTA 57.056 29.630 0.00 0.00 39.71 1.98
586 595 7.500992 TGAGATATAGTTTGGTCTCATTCACC 58.499 38.462 0.16 0.00 41.40 4.02
587 596 7.345653 TGAGATATAGTTTGGTCTCATTCACCT 59.654 37.037 0.16 0.00 41.40 4.00
588 597 8.095452 AGATATAGTTTGGTCTCATTCACCTT 57.905 34.615 0.00 0.00 34.66 3.50
589 598 8.552296 AGATATAGTTTGGTCTCATTCACCTTT 58.448 33.333 0.00 0.00 34.66 3.11
590 599 9.178758 GATATAGTTTGGTCTCATTCACCTTTT 57.821 33.333 0.00 0.00 34.66 2.27
594 603 8.567285 AGTTTGGTCTCATTCACCTTTTATAG 57.433 34.615 0.00 0.00 34.66 1.31
595 604 7.121315 AGTTTGGTCTCATTCACCTTTTATAGC 59.879 37.037 0.00 0.00 34.66 2.97
596 605 6.313519 TGGTCTCATTCACCTTTTATAGCT 57.686 37.500 0.00 0.00 34.66 3.32
597 606 7.432148 TGGTCTCATTCACCTTTTATAGCTA 57.568 36.000 0.00 0.00 34.66 3.32
598 607 8.034313 TGGTCTCATTCACCTTTTATAGCTAT 57.966 34.615 11.77 11.77 34.66 2.97
599 608 8.494433 TGGTCTCATTCACCTTTTATAGCTATT 58.506 33.333 12.39 0.00 34.66 1.73
600 609 8.778358 GGTCTCATTCACCTTTTATAGCTATTG 58.222 37.037 12.39 2.96 0.00 1.90
601 610 8.778358 GTCTCATTCACCTTTTATAGCTATTGG 58.222 37.037 12.39 11.49 0.00 3.16
602 611 8.713971 TCTCATTCACCTTTTATAGCTATTGGA 58.286 33.333 12.39 0.00 0.00 3.53
603 612 9.512588 CTCATTCACCTTTTATAGCTATTGGAT 57.487 33.333 12.39 0.01 0.00 3.41
604 613 9.288576 TCATTCACCTTTTATAGCTATTGGATG 57.711 33.333 12.39 12.74 0.00 3.51
605 614 9.071276 CATTCACCTTTTATAGCTATTGGATGT 57.929 33.333 12.39 2.05 0.00 3.06
606 615 8.450578 TTCACCTTTTATAGCTATTGGATGTG 57.549 34.615 12.39 13.69 0.00 3.21
607 616 7.801104 TCACCTTTTATAGCTATTGGATGTGA 58.199 34.615 12.39 15.55 0.00 3.58
608 617 8.439971 TCACCTTTTATAGCTATTGGATGTGAT 58.560 33.333 12.39 0.00 0.00 3.06
609 618 8.509690 CACCTTTTATAGCTATTGGATGTGATG 58.490 37.037 12.39 0.40 0.00 3.07
610 619 7.175641 ACCTTTTATAGCTATTGGATGTGATGC 59.824 37.037 12.39 0.00 0.00 3.91
611 620 7.392673 CCTTTTATAGCTATTGGATGTGATGCT 59.607 37.037 12.39 0.00 0.00 3.79
612 621 9.440773 CTTTTATAGCTATTGGATGTGATGCTA 57.559 33.333 12.39 0.00 36.26 3.49
613 622 9.964354 TTTTATAGCTATTGGATGTGATGCTAT 57.036 29.630 12.39 0.00 42.49 2.97
617 626 7.250032 AGCTATTGGATGTGATGCTATAAGA 57.750 36.000 0.00 0.00 0.00 2.10
618 627 7.859540 AGCTATTGGATGTGATGCTATAAGAT 58.140 34.615 0.00 0.00 0.00 2.40
619 628 7.769507 AGCTATTGGATGTGATGCTATAAGATG 59.230 37.037 0.00 0.00 0.00 2.90
620 629 6.754702 ATTGGATGTGATGCTATAAGATGC 57.245 37.500 0.00 0.00 0.00 3.91
621 630 4.248058 TGGATGTGATGCTATAAGATGCG 58.752 43.478 0.00 0.00 0.00 4.73
622 631 4.248859 GGATGTGATGCTATAAGATGCGT 58.751 43.478 0.00 0.00 0.00 5.24
623 632 4.092529 GGATGTGATGCTATAAGATGCGTG 59.907 45.833 0.00 0.00 0.00 5.34
624 633 4.058721 TGTGATGCTATAAGATGCGTGT 57.941 40.909 0.00 0.00 0.00 4.49
625 634 5.195001 TGTGATGCTATAAGATGCGTGTA 57.805 39.130 0.00 0.00 0.00 2.90
626 635 5.783111 TGTGATGCTATAAGATGCGTGTAT 58.217 37.500 0.00 0.00 0.00 2.29
627 636 5.634859 TGTGATGCTATAAGATGCGTGTATG 59.365 40.000 0.00 0.00 0.00 2.39
628 637 4.627035 TGATGCTATAAGATGCGTGTATGC 59.373 41.667 0.00 0.00 0.00 3.14
629 638 4.257267 TGCTATAAGATGCGTGTATGCT 57.743 40.909 0.00 0.00 35.36 3.79
630 639 3.989817 TGCTATAAGATGCGTGTATGCTG 59.010 43.478 0.00 0.00 35.36 4.41
631 640 4.237724 GCTATAAGATGCGTGTATGCTGA 58.762 43.478 0.00 0.00 35.36 4.26
632 641 4.090642 GCTATAAGATGCGTGTATGCTGAC 59.909 45.833 0.00 0.00 35.36 3.51
633 642 1.280982 AAGATGCGTGTATGCTGACG 58.719 50.000 0.00 0.00 38.63 4.35
634 643 0.173481 AGATGCGTGTATGCTGACGT 59.827 50.000 0.00 0.00 37.89 4.34
635 644 0.298707 GATGCGTGTATGCTGACGTG 59.701 55.000 0.00 0.00 37.89 4.49
636 645 1.083806 ATGCGTGTATGCTGACGTGG 61.084 55.000 0.00 0.00 37.89 4.94
637 646 2.452813 GCGTGTATGCTGACGTGGG 61.453 63.158 0.00 0.00 37.89 4.61
638 647 1.080093 CGTGTATGCTGACGTGGGT 60.080 57.895 0.00 0.00 0.00 4.51
639 648 0.669318 CGTGTATGCTGACGTGGGTT 60.669 55.000 0.00 0.00 0.00 4.11
640 649 0.796312 GTGTATGCTGACGTGGGTTG 59.204 55.000 0.00 0.00 0.00 3.77
641 650 0.394938 TGTATGCTGACGTGGGTTGT 59.605 50.000 0.00 0.00 0.00 3.32
642 651 1.619332 TGTATGCTGACGTGGGTTGTA 59.381 47.619 0.00 0.00 0.00 2.41
643 652 2.235155 TGTATGCTGACGTGGGTTGTAT 59.765 45.455 0.00 0.00 0.00 2.29
644 653 2.489938 ATGCTGACGTGGGTTGTATT 57.510 45.000 0.00 0.00 0.00 1.89
645 654 2.264005 TGCTGACGTGGGTTGTATTT 57.736 45.000 0.00 0.00 0.00 1.40
646 655 1.876799 TGCTGACGTGGGTTGTATTTG 59.123 47.619 0.00 0.00 0.00 2.32
647 656 1.877443 GCTGACGTGGGTTGTATTTGT 59.123 47.619 0.00 0.00 0.00 2.83
648 657 2.292292 GCTGACGTGGGTTGTATTTGTT 59.708 45.455 0.00 0.00 0.00 2.83
649 658 3.243267 GCTGACGTGGGTTGTATTTGTTT 60.243 43.478 0.00 0.00 0.00 2.83
650 659 4.735283 GCTGACGTGGGTTGTATTTGTTTT 60.735 41.667 0.00 0.00 0.00 2.43
651 660 5.326200 TGACGTGGGTTGTATTTGTTTTT 57.674 34.783 0.00 0.00 0.00 1.94
652 661 5.103000 TGACGTGGGTTGTATTTGTTTTTG 58.897 37.500 0.00 0.00 0.00 2.44
653 662 5.074584 ACGTGGGTTGTATTTGTTTTTGT 57.925 34.783 0.00 0.00 0.00 2.83
654 663 5.480205 ACGTGGGTTGTATTTGTTTTTGTT 58.520 33.333 0.00 0.00 0.00 2.83
655 664 5.932883 ACGTGGGTTGTATTTGTTTTTGTTT 59.067 32.000 0.00 0.00 0.00 2.83
656 665 6.427242 ACGTGGGTTGTATTTGTTTTTGTTTT 59.573 30.769 0.00 0.00 0.00 2.43
657 666 6.956520 CGTGGGTTGTATTTGTTTTTGTTTTC 59.043 34.615 0.00 0.00 0.00 2.29
658 667 7.360101 CGTGGGTTGTATTTGTTTTTGTTTTCA 60.360 33.333 0.00 0.00 0.00 2.69
659 668 8.290325 GTGGGTTGTATTTGTTTTTGTTTTCAA 58.710 29.630 0.00 0.00 38.10 2.69
660 669 8.846211 TGGGTTGTATTTGTTTTTGTTTTCAAA 58.154 25.926 0.00 0.00 46.39 2.69
673 682 6.522625 TTGTTTTCAAAGTGAATGAGACCA 57.477 33.333 0.00 0.00 36.11 4.02
674 683 6.522625 TGTTTTCAAAGTGAATGAGACCAA 57.477 33.333 0.00 0.00 36.11 3.67
675 684 6.929625 TGTTTTCAAAGTGAATGAGACCAAA 58.070 32.000 0.00 0.00 36.11 3.28
676 685 7.555087 TGTTTTCAAAGTGAATGAGACCAAAT 58.445 30.769 0.00 0.00 36.11 2.32
677 686 8.040132 TGTTTTCAAAGTGAATGAGACCAAATT 58.960 29.630 0.00 0.00 36.11 1.82
678 687 9.528018 GTTTTCAAAGTGAATGAGACCAAATTA 57.472 29.630 0.00 0.00 36.11 1.40
737 746 2.773993 ATTGGGCAATCTGGCTTTTG 57.226 45.000 0.00 0.00 43.20 2.44
740 749 0.390735 GGGCAATCTGGCTTTTGCTG 60.391 55.000 15.50 0.00 45.81 4.41
743 752 1.259609 CAATCTGGCTTTTGCTGGGA 58.740 50.000 0.00 0.00 46.54 4.37
754 763 6.712532 GCTTTTGCTGGGATTTCCATCCTG 62.713 50.000 0.00 0.00 46.01 3.86
764 773 2.505650 TTCCATCCTGCCATTTCGAA 57.494 45.000 0.00 0.00 0.00 3.71
766 775 2.801483 TCCATCCTGCCATTTCGAAAA 58.199 42.857 15.66 0.00 0.00 2.29
878 888 5.806366 ATTCGTGAAAACGGTAAATAGGG 57.194 39.130 0.00 0.00 0.00 3.53
923 934 2.025887 ACAGCCTGGGATTTAGAGTTGG 60.026 50.000 0.00 0.00 0.00 3.77
970 981 3.064207 CGTCGTCATTTTCTTCCTTGGA 58.936 45.455 0.00 0.00 0.00 3.53
971 982 3.123621 CGTCGTCATTTTCTTCCTTGGAG 59.876 47.826 0.00 0.00 0.00 3.86
973 984 3.326588 TCGTCATTTTCTTCCTTGGAGGA 59.673 43.478 0.00 0.00 44.10 3.71
975 986 4.083271 CGTCATTTTCTTCCTTGGAGGAAC 60.083 45.833 12.79 2.89 46.88 3.62
976 987 4.827284 GTCATTTTCTTCCTTGGAGGAACA 59.173 41.667 12.79 8.03 46.88 3.18
977 988 5.048434 GTCATTTTCTTCCTTGGAGGAACAG 60.048 44.000 12.79 7.06 46.88 3.16
978 989 3.508845 TTTCTTCCTTGGAGGAACAGG 57.491 47.619 12.79 0.00 46.88 4.00
979 990 1.362224 TCTTCCTTGGAGGAACAGGG 58.638 55.000 5.33 0.00 46.88 4.45
980 991 0.329596 CTTCCTTGGAGGAACAGGGG 59.670 60.000 5.33 0.00 46.88 4.79
981 992 0.104144 TTCCTTGGAGGAACAGGGGA 60.104 55.000 5.33 0.00 46.88 4.81
982 993 0.547712 TCCTTGGAGGAACAGGGGAG 60.548 60.000 0.00 0.00 42.51 4.30
983 994 1.566298 CCTTGGAGGAACAGGGGAGG 61.566 65.000 0.00 0.00 37.67 4.30
984 995 1.541368 TTGGAGGAACAGGGGAGGG 60.541 63.158 0.00 0.00 0.00 4.30
985 996 2.692741 GGAGGAACAGGGGAGGGG 60.693 72.222 0.00 0.00 0.00 4.79
986 997 2.692741 GAGGAACAGGGGAGGGGG 60.693 72.222 0.00 0.00 0.00 5.40
987 998 3.216371 AGGAACAGGGGAGGGGGA 61.216 66.667 0.00 0.00 0.00 4.81
988 999 2.692741 GGAACAGGGGAGGGGGAG 60.693 72.222 0.00 0.00 0.00 4.30
1192 1217 1.077625 TTAACCATGCACCCACCCC 59.922 57.895 0.00 0.00 0.00 4.95
1206 1231 0.394216 CACCCCATTTCCTGCGATCA 60.394 55.000 0.00 0.00 0.00 2.92
1217 1242 2.636403 TCCTGCGATCAATCCATCATCT 59.364 45.455 0.00 0.00 0.00 2.90
1250 1275 2.555123 TCGCAGAGCCATTGTTTCC 58.445 52.632 0.00 0.00 0.00 3.13
1699 1737 2.126189 GACTACGTCACCGGCACC 60.126 66.667 0.00 0.00 38.78 5.01
1908 1949 4.542075 GGAACGAGGGAAGGATGC 57.458 61.111 0.00 0.00 0.00 3.91
1914 1955 1.835693 GAGGGAAGGATGCAGGAGG 59.164 63.158 0.00 0.00 0.00 4.30
2005 2046 5.482175 ACTGATTATAGATGGCTAGTGTCCC 59.518 44.000 0.00 0.00 0.00 4.46
2023 2064 4.836736 TGTCCCCTATAAATTACTCCCTCG 59.163 45.833 0.00 0.00 0.00 4.63
2047 2088 5.353938 GTCCCATAATGTAAACGTCTAGCA 58.646 41.667 0.00 0.00 0.00 3.49
2048 2089 5.989777 GTCCCATAATGTAAACGTCTAGCAT 59.010 40.000 0.00 0.00 0.00 3.79
2049 2090 6.482308 GTCCCATAATGTAAACGTCTAGCATT 59.518 38.462 10.73 10.73 34.62 3.56
2050 2091 7.654520 GTCCCATAATGTAAACGTCTAGCATTA 59.345 37.037 13.32 13.32 36.74 1.90
2051 2092 8.372459 TCCCATAATGTAAACGTCTAGCATTAT 58.628 33.333 15.52 15.52 40.94 1.28
2114 2155 8.437742 GCATCTTCAGTAAATGGTTCAAATTTG 58.562 33.333 12.15 12.15 0.00 2.32
2115 2156 9.695526 CATCTTCAGTAAATGGTTCAAATTTGA 57.304 29.630 16.91 16.91 34.92 2.69
2127 2169 4.993029 TCAAATTTGACGGTCCAAAACT 57.007 36.364 16.91 0.00 39.20 2.66
2185 2227 0.440371 GAGCTCCGAAAAACGCTCAG 59.560 55.000 0.87 0.00 46.06 3.35
2198 2240 0.108472 CGCTCAGCTCCAACAGATGA 60.108 55.000 0.00 0.00 45.59 2.92
2270 2312 7.865385 CCAAAGATGTAAAAATCTGAAAACGGA 59.135 33.333 0.00 0.00 36.99 4.69
2415 2461 3.634397 TCCCTCTACCAAAAGAGCATG 57.366 47.619 0.00 0.00 41.48 4.06
2602 2649 1.131126 CGGAAGCATCTTCATTGCGTT 59.869 47.619 8.59 0.00 44.82 4.84
2719 2769 1.526917 CCTCCCATGCCGCTAAAGG 60.527 63.158 0.00 0.00 0.00 3.11
2746 2817 1.304381 ATGTTGCCACCGAAGCCAT 60.304 52.632 0.00 0.00 0.00 4.40
2750 2821 1.841302 TTGCCACCGAAGCCATCTCT 61.841 55.000 0.00 0.00 0.00 3.10
2831 2902 2.367512 ACCTCCCATGCCTCCTCC 60.368 66.667 0.00 0.00 0.00 4.30
2832 2903 3.174265 CCTCCCATGCCTCCTCCC 61.174 72.222 0.00 0.00 0.00 4.30
2833 2904 2.367377 CTCCCATGCCTCCTCCCA 60.367 66.667 0.00 0.00 0.00 4.37
2834 2905 1.773391 CTCCCATGCCTCCTCCCAT 60.773 63.158 0.00 0.00 0.00 4.00
2835 2906 0.474466 CTCCCATGCCTCCTCCCATA 60.474 60.000 0.00 0.00 0.00 2.74
2836 2907 0.474466 TCCCATGCCTCCTCCCATAG 60.474 60.000 0.00 0.00 0.00 2.23
2837 2908 1.377994 CCATGCCTCCTCCCATAGC 59.622 63.158 0.00 0.00 0.00 2.97
2838 2909 1.421346 CCATGCCTCCTCCCATAGCA 61.421 60.000 0.00 0.00 37.94 3.49
2839 2910 0.250640 CATGCCTCCTCCCATAGCAC 60.251 60.000 0.00 0.00 36.06 4.40
2840 2911 1.422161 ATGCCTCCTCCCATAGCACC 61.422 60.000 0.00 0.00 36.06 5.01
2841 2912 1.768077 GCCTCCTCCCATAGCACCT 60.768 63.158 0.00 0.00 0.00 4.00
2842 2913 1.763546 GCCTCCTCCCATAGCACCTC 61.764 65.000 0.00 0.00 0.00 3.85
2883 3014 0.474466 CTCCCATGCCTCCTCCCATA 60.474 60.000 0.00 0.00 0.00 2.74
2884 3015 0.196888 TCCCATGCCTCCTCCCATAT 59.803 55.000 0.00 0.00 0.00 1.78
2887 3018 1.991070 CCATGCCTCCTCCCATATTCT 59.009 52.381 0.00 0.00 0.00 2.40
2888 3019 2.377869 CCATGCCTCCTCCCATATTCTT 59.622 50.000 0.00 0.00 0.00 2.52
2889 3020 3.588842 CCATGCCTCCTCCCATATTCTTA 59.411 47.826 0.00 0.00 0.00 2.10
2927 4153 4.868314 TCATCATTTGCCACATTTGTCA 57.132 36.364 0.00 0.00 0.00 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.788191 AAGGACGAAGCGCTTGGGAG 62.788 60.000 31.41 19.87 0.00 4.30
5 6 1.374758 CTCCAAGGACGAAGCGCTT 60.375 57.895 25.35 25.35 0.00 4.68
30 31 0.038744 CACTGGTCCCTCTTGCCAAT 59.961 55.000 0.00 0.00 0.00 3.16
32 33 2.528818 CCACTGGTCCCTCTTGCCA 61.529 63.158 0.00 0.00 0.00 4.92
36 37 0.119155 TCCATCCACTGGTCCCTCTT 59.881 55.000 0.00 0.00 46.08 2.85
40 41 0.035056 CAACTCCATCCACTGGTCCC 60.035 60.000 0.00 0.00 46.08 4.46
54 55 1.202486 TCTCGACACCAACACCAACTC 60.202 52.381 0.00 0.00 0.00 3.01
74 75 1.609061 CCTCATCGTTGCCACAGAAGT 60.609 52.381 0.00 0.00 0.00 3.01
101 102 0.243636 CCTCAACCAAAACCATCGCC 59.756 55.000 0.00 0.00 0.00 5.54
104 105 4.394729 TGACTACCTCAACCAAAACCATC 58.605 43.478 0.00 0.00 0.00 3.51
149 150 2.875296 ACAAACCAGCTAAGGCAATCA 58.125 42.857 0.00 0.00 41.70 2.57
158 159 4.461081 ACTTTCACAACAACAAACCAGCTA 59.539 37.500 0.00 0.00 0.00 3.32
160 161 3.584834 ACTTTCACAACAACAAACCAGC 58.415 40.909 0.00 0.00 0.00 4.85
175 176 1.536766 CCAATGCAGCTTCGACTTTCA 59.463 47.619 0.00 0.00 0.00 2.69
177 178 1.267806 CACCAATGCAGCTTCGACTTT 59.732 47.619 0.00 0.00 0.00 2.66
191 192 2.547595 CCACTGGGACCCCACCAAT 61.548 63.158 8.45 0.00 41.89 3.16
192 193 3.182263 CCACTGGGACCCCACCAA 61.182 66.667 8.45 0.00 41.89 3.67
212 213 2.278596 CTACCGCCCGTCATCGTG 60.279 66.667 0.00 0.00 35.01 4.35
222 223 2.033602 AACCAACCAGCTACCGCC 59.966 61.111 0.00 0.00 36.60 6.13
223 224 2.388232 CGAACCAACCAGCTACCGC 61.388 63.158 0.00 0.00 0.00 5.68
225 226 0.872388 CAACGAACCAACCAGCTACC 59.128 55.000 0.00 0.00 0.00 3.18
227 228 2.301870 AGATCAACGAACCAACCAGCTA 59.698 45.455 0.00 0.00 0.00 3.32
229 230 1.523758 AGATCAACGAACCAACCAGC 58.476 50.000 0.00 0.00 0.00 4.85
230 231 2.878406 ACAAGATCAACGAACCAACCAG 59.122 45.455 0.00 0.00 0.00 4.00
236 237 1.392510 GCCGTACAAGATCAACGAACC 59.607 52.381 10.32 0.00 38.89 3.62
267 268 5.044558 GCAGAACTACGAAGGAGAATTAGG 58.955 45.833 0.00 0.00 0.00 2.69
286 287 3.443925 CTCCGGCTCTGACGCAGA 61.444 66.667 0.00 8.83 38.25 4.26
289 290 4.742201 TTGCTCCGGCTCTGACGC 62.742 66.667 0.00 0.00 39.59 5.19
306 307 0.655733 CACTTGCGACCAGAAAACGT 59.344 50.000 0.00 0.00 0.00 3.99
308 309 1.021968 ACCACTTGCGACCAGAAAAC 58.978 50.000 0.00 0.00 0.00 2.43
311 312 0.179234 TCAACCACTTGCGACCAGAA 59.821 50.000 0.00 0.00 0.00 3.02
318 319 1.442520 CGCCATTCAACCACTTGCG 60.443 57.895 0.00 0.00 0.00 4.85
331 332 0.248012 TGTACAACGATCCACGCCAT 59.752 50.000 0.00 0.00 46.94 4.40
336 337 1.067142 TGGAGCTGTACAACGATCCAC 60.067 52.381 15.86 0.00 32.04 4.02
342 343 1.078709 CCATGTGGAGCTGTACAACG 58.921 55.000 0.00 0.00 37.39 4.10
345 346 1.550524 GAGACCATGTGGAGCTGTACA 59.449 52.381 5.96 0.00 38.94 2.90
346 347 1.827969 AGAGACCATGTGGAGCTGTAC 59.172 52.381 5.96 0.00 38.94 2.90
351 352 3.639094 ACACTATAGAGACCATGTGGAGC 59.361 47.826 6.78 0.00 38.94 4.70
381 382 3.752412 TCGTCGTAAGTGATTGTCGAT 57.248 42.857 0.00 0.00 39.48 3.59
387 388 4.215827 ACTCTGACTTCGTCGTAAGTGATT 59.784 41.667 12.69 0.99 39.78 2.57
388 389 3.752222 ACTCTGACTTCGTCGTAAGTGAT 59.248 43.478 12.69 0.00 39.78 3.06
391 392 2.157279 CGACTCTGACTTCGTCGTAAGT 59.843 50.000 8.49 9.02 43.82 2.24
414 415 4.404394 TCGTCATACCTAAATCCTCAGCAA 59.596 41.667 0.00 0.00 0.00 3.91
419 420 5.927115 GGTTCATCGTCATACCTAAATCCTC 59.073 44.000 0.00 0.00 0.00 3.71
428 429 2.627945 TGCAAGGTTCATCGTCATACC 58.372 47.619 0.00 0.00 0.00 2.73
437 438 2.211250 AGACAGCATGCAAGGTTCAT 57.789 45.000 21.98 3.03 42.53 2.57
441 442 1.530013 GCCAAGACAGCATGCAAGGT 61.530 55.000 21.98 14.83 42.53 3.50
442 443 1.214589 GCCAAGACAGCATGCAAGG 59.785 57.895 21.98 11.43 42.53 3.61
444 445 1.171549 TTCGCCAAGACAGCATGCAA 61.172 50.000 21.98 0.00 42.53 4.08
447 448 0.957395 ACCTTCGCCAAGACAGCATG 60.957 55.000 0.00 0.00 46.00 4.06
448 449 0.674895 GACCTTCGCCAAGACAGCAT 60.675 55.000 0.00 0.00 0.00 3.79
451 452 1.884235 AAAGACCTTCGCCAAGACAG 58.116 50.000 0.00 0.00 0.00 3.51
457 458 1.133915 ACTCCAAAAAGACCTTCGCCA 60.134 47.619 0.00 0.00 0.00 5.69
458 459 1.266989 CACTCCAAAAAGACCTTCGCC 59.733 52.381 0.00 0.00 0.00 5.54
460 461 2.290641 CACCACTCCAAAAAGACCTTCG 59.709 50.000 0.00 0.00 0.00 3.79
461 462 3.066760 CACACCACTCCAAAAAGACCTTC 59.933 47.826 0.00 0.00 0.00 3.46
466 467 1.748493 GCACACACCACTCCAAAAAGA 59.252 47.619 0.00 0.00 0.00 2.52
468 469 1.476085 CTGCACACACCACTCCAAAAA 59.524 47.619 0.00 0.00 0.00 1.94
473 474 0.679505 TACTCTGCACACACCACTCC 59.320 55.000 0.00 0.00 0.00 3.85
474 475 2.232452 AGATACTCTGCACACACCACTC 59.768 50.000 0.00 0.00 0.00 3.51
481 482 4.033358 GCACATACAAGATACTCTGCACAC 59.967 45.833 0.00 0.00 0.00 3.82
520 529 9.953697 AGCAAAACTGTTAATTAAAACGTGATA 57.046 25.926 0.00 0.00 31.76 2.15
521 530 8.865590 AGCAAAACTGTTAATTAAAACGTGAT 57.134 26.923 0.00 0.00 31.76 3.06
531 540 9.289782 AGATGAGTTCTAGCAAAACTGTTAATT 57.710 29.630 0.32 0.00 37.10 1.40
532 541 8.854614 AGATGAGTTCTAGCAAAACTGTTAAT 57.145 30.769 0.32 0.00 37.10 1.40
533 542 9.424319 CTAGATGAGTTCTAGCAAAACTGTTAA 57.576 33.333 0.32 0.00 45.63 2.01
534 543 8.988064 CTAGATGAGTTCTAGCAAAACTGTTA 57.012 34.615 0.32 0.00 45.63 2.41
535 544 7.897575 CTAGATGAGTTCTAGCAAAACTGTT 57.102 36.000 0.32 0.00 45.63 3.16
562 571 7.731054 AGGTGAATGAGACCAAACTATATCTC 58.269 38.462 0.00 0.00 38.46 2.75
563 572 7.682787 AGGTGAATGAGACCAAACTATATCT 57.317 36.000 0.00 0.00 35.76 1.98
564 573 8.738645 AAAGGTGAATGAGACCAAACTATATC 57.261 34.615 0.00 0.00 35.76 1.63
568 577 9.667107 CTATAAAAGGTGAATGAGACCAAACTA 57.333 33.333 0.00 0.00 35.76 2.24
569 578 7.121315 GCTATAAAAGGTGAATGAGACCAAACT 59.879 37.037 0.00 0.00 35.76 2.66
570 579 7.121315 AGCTATAAAAGGTGAATGAGACCAAAC 59.879 37.037 0.00 0.00 35.76 2.93
571 580 7.175104 AGCTATAAAAGGTGAATGAGACCAAA 58.825 34.615 0.00 0.00 35.76 3.28
572 581 6.721318 AGCTATAAAAGGTGAATGAGACCAA 58.279 36.000 0.00 0.00 35.76 3.67
573 582 6.313519 AGCTATAAAAGGTGAATGAGACCA 57.686 37.500 0.00 0.00 35.76 4.02
574 583 8.778358 CAATAGCTATAAAAGGTGAATGAGACC 58.222 37.037 6.68 0.00 37.13 3.85
575 584 8.778358 CCAATAGCTATAAAAGGTGAATGAGAC 58.222 37.037 6.68 0.00 37.13 3.36
576 585 8.713971 TCCAATAGCTATAAAAGGTGAATGAGA 58.286 33.333 6.68 0.00 37.13 3.27
577 586 8.908786 TCCAATAGCTATAAAAGGTGAATGAG 57.091 34.615 6.68 0.00 37.13 2.90
578 587 9.288576 CATCCAATAGCTATAAAAGGTGAATGA 57.711 33.333 6.68 0.00 37.13 2.57
579 588 9.071276 ACATCCAATAGCTATAAAAGGTGAATG 57.929 33.333 6.68 2.73 37.13 2.67
580 589 9.071276 CACATCCAATAGCTATAAAAGGTGAAT 57.929 33.333 6.68 0.00 37.13 2.57
581 590 8.271458 TCACATCCAATAGCTATAAAAGGTGAA 58.729 33.333 19.05 9.24 37.13 3.18
582 591 7.801104 TCACATCCAATAGCTATAAAAGGTGA 58.199 34.615 18.13 18.13 37.13 4.02
583 592 8.509690 CATCACATCCAATAGCTATAAAAGGTG 58.490 37.037 6.68 12.40 37.13 4.00
584 593 7.175641 GCATCACATCCAATAGCTATAAAAGGT 59.824 37.037 6.68 0.39 39.81 3.50
585 594 7.392673 AGCATCACATCCAATAGCTATAAAAGG 59.607 37.037 6.68 7.31 0.00 3.11
586 595 8.332996 AGCATCACATCCAATAGCTATAAAAG 57.667 34.615 6.68 0.00 0.00 2.27
587 596 9.964354 ATAGCATCACATCCAATAGCTATAAAA 57.036 29.630 6.68 0.00 40.75 1.52
591 600 8.985922 TCTTATAGCATCACATCCAATAGCTAT 58.014 33.333 0.00 0.00 43.70 2.97
592 601 8.366359 TCTTATAGCATCACATCCAATAGCTA 57.634 34.615 0.00 0.00 37.49 3.32
593 602 7.250032 TCTTATAGCATCACATCCAATAGCT 57.750 36.000 0.00 0.00 34.84 3.32
594 603 7.466996 GCATCTTATAGCATCACATCCAATAGC 60.467 40.741 0.00 0.00 0.00 2.97
595 604 7.254353 CGCATCTTATAGCATCACATCCAATAG 60.254 40.741 0.00 0.00 0.00 1.73
596 605 6.536224 CGCATCTTATAGCATCACATCCAATA 59.464 38.462 0.00 0.00 0.00 1.90
597 606 5.353400 CGCATCTTATAGCATCACATCCAAT 59.647 40.000 0.00 0.00 0.00 3.16
598 607 4.692155 CGCATCTTATAGCATCACATCCAA 59.308 41.667 0.00 0.00 0.00 3.53
599 608 4.248058 CGCATCTTATAGCATCACATCCA 58.752 43.478 0.00 0.00 0.00 3.41
600 609 4.092529 CACGCATCTTATAGCATCACATCC 59.907 45.833 0.00 0.00 0.00 3.51
601 610 4.687948 ACACGCATCTTATAGCATCACATC 59.312 41.667 0.00 0.00 0.00 3.06
602 611 4.635223 ACACGCATCTTATAGCATCACAT 58.365 39.130 0.00 0.00 0.00 3.21
603 612 4.058721 ACACGCATCTTATAGCATCACA 57.941 40.909 0.00 0.00 0.00 3.58
604 613 5.445142 GCATACACGCATCTTATAGCATCAC 60.445 44.000 0.00 0.00 0.00 3.06
605 614 4.627035 GCATACACGCATCTTATAGCATCA 59.373 41.667 0.00 0.00 0.00 3.07
606 615 4.867047 AGCATACACGCATCTTATAGCATC 59.133 41.667 0.00 0.00 0.00 3.91
607 616 4.628766 CAGCATACACGCATCTTATAGCAT 59.371 41.667 0.00 0.00 0.00 3.79
608 617 3.989817 CAGCATACACGCATCTTATAGCA 59.010 43.478 0.00 0.00 0.00 3.49
609 618 4.090642 GTCAGCATACACGCATCTTATAGC 59.909 45.833 0.00 0.00 0.00 2.97
610 619 4.322009 CGTCAGCATACACGCATCTTATAG 59.678 45.833 0.00 0.00 0.00 1.31
611 620 4.226761 CGTCAGCATACACGCATCTTATA 58.773 43.478 0.00 0.00 0.00 0.98
612 621 3.052745 CGTCAGCATACACGCATCTTAT 58.947 45.455 0.00 0.00 0.00 1.73
613 622 2.159296 ACGTCAGCATACACGCATCTTA 60.159 45.455 0.00 0.00 39.73 2.10
614 623 1.280982 CGTCAGCATACACGCATCTT 58.719 50.000 0.00 0.00 0.00 2.40
615 624 0.173481 ACGTCAGCATACACGCATCT 59.827 50.000 0.00 0.00 39.73 2.90
616 625 0.298707 CACGTCAGCATACACGCATC 59.701 55.000 0.00 0.00 39.73 3.91
617 626 1.083806 CCACGTCAGCATACACGCAT 61.084 55.000 0.00 0.00 39.73 4.73
618 627 1.736282 CCACGTCAGCATACACGCA 60.736 57.895 0.00 0.00 39.73 5.24
619 628 2.452813 CCCACGTCAGCATACACGC 61.453 63.158 0.00 0.00 39.73 5.34
620 629 0.669318 AACCCACGTCAGCATACACG 60.669 55.000 0.00 0.00 41.90 4.49
621 630 0.796312 CAACCCACGTCAGCATACAC 59.204 55.000 0.00 0.00 0.00 2.90
622 631 0.394938 ACAACCCACGTCAGCATACA 59.605 50.000 0.00 0.00 0.00 2.29
623 632 2.373540 TACAACCCACGTCAGCATAC 57.626 50.000 0.00 0.00 0.00 2.39
624 633 3.620427 AATACAACCCACGTCAGCATA 57.380 42.857 0.00 0.00 0.00 3.14
625 634 2.487762 CAAATACAACCCACGTCAGCAT 59.512 45.455 0.00 0.00 0.00 3.79
626 635 1.876799 CAAATACAACCCACGTCAGCA 59.123 47.619 0.00 0.00 0.00 4.41
627 636 1.877443 ACAAATACAACCCACGTCAGC 59.123 47.619 0.00 0.00 0.00 4.26
628 637 4.561735 AAACAAATACAACCCACGTCAG 57.438 40.909 0.00 0.00 0.00 3.51
629 638 4.985538 AAAACAAATACAACCCACGTCA 57.014 36.364 0.00 0.00 0.00 4.35
630 639 5.103687 ACAAAAACAAATACAACCCACGTC 58.896 37.500 0.00 0.00 0.00 4.34
631 640 5.074584 ACAAAAACAAATACAACCCACGT 57.925 34.783 0.00 0.00 0.00 4.49
632 641 6.410243 AAACAAAAACAAATACAACCCACG 57.590 33.333 0.00 0.00 0.00 4.94
633 642 7.807680 TGAAAACAAAAACAAATACAACCCAC 58.192 30.769 0.00 0.00 0.00 4.61
634 643 7.979444 TGAAAACAAAAACAAATACAACCCA 57.021 28.000 0.00 0.00 0.00 4.51
635 644 9.335891 CTTTGAAAACAAAAACAAATACAACCC 57.664 29.630 0.00 0.00 33.01 4.11
636 645 9.885934 ACTTTGAAAACAAAAACAAATACAACC 57.114 25.926 0.00 0.00 33.01 3.77
643 652 9.875675 CTCATTCACTTTGAAAACAAAAACAAA 57.124 25.926 0.00 0.00 40.12 2.83
644 653 9.265901 TCTCATTCACTTTGAAAACAAAAACAA 57.734 25.926 0.00 0.00 40.12 2.83
645 654 8.707839 GTCTCATTCACTTTGAAAACAAAAACA 58.292 29.630 0.00 0.00 40.12 2.83
646 655 8.168626 GGTCTCATTCACTTTGAAAACAAAAAC 58.831 33.333 0.00 0.00 40.12 2.43
647 656 7.875041 TGGTCTCATTCACTTTGAAAACAAAAA 59.125 29.630 0.00 0.00 40.12 1.94
648 657 7.382110 TGGTCTCATTCACTTTGAAAACAAAA 58.618 30.769 0.00 0.00 40.12 2.44
649 658 6.929625 TGGTCTCATTCACTTTGAAAACAAA 58.070 32.000 0.00 0.00 40.12 2.83
650 659 6.522625 TGGTCTCATTCACTTTGAAAACAA 57.477 33.333 0.00 0.00 40.12 2.83
651 660 6.522625 TTGGTCTCATTCACTTTGAAAACA 57.477 33.333 0.00 0.00 40.12 2.83
652 661 8.424274 AATTTGGTCTCATTCACTTTGAAAAC 57.576 30.769 0.00 0.00 40.12 2.43
689 698 9.890915 ATTAAAGGGAGTATCTAGAACTCATCT 57.109 33.333 24.15 19.65 44.25 2.90
698 707 9.232473 GCCCAATTAATTAAAGGGAGTATCTAG 57.768 37.037 29.55 10.76 36.98 2.43
699 708 8.729047 TGCCCAATTAATTAAAGGGAGTATCTA 58.271 33.333 29.55 12.20 36.98 1.98
700 709 7.591821 TGCCCAATTAATTAAAGGGAGTATCT 58.408 34.615 29.55 0.27 36.98 1.98
701 710 7.833285 TGCCCAATTAATTAAAGGGAGTATC 57.167 36.000 29.55 17.90 36.98 2.24
702 711 8.797436 ATTGCCCAATTAATTAAAGGGAGTAT 57.203 30.769 29.55 19.70 36.98 2.12
703 712 8.065007 AGATTGCCCAATTAATTAAAGGGAGTA 58.935 33.333 29.55 18.80 36.98 2.59
704 713 6.902974 AGATTGCCCAATTAATTAAAGGGAGT 59.097 34.615 29.55 17.20 36.98 3.85
705 714 7.212274 CAGATTGCCCAATTAATTAAAGGGAG 58.788 38.462 29.55 16.62 36.98 4.30
706 715 6.099557 CCAGATTGCCCAATTAATTAAAGGGA 59.900 38.462 29.55 17.80 36.98 4.20
707 716 6.290605 CCAGATTGCCCAATTAATTAAAGGG 58.709 40.000 24.57 24.57 37.53 3.95
708 717 5.759763 GCCAGATTGCCCAATTAATTAAAGG 59.240 40.000 1.21 7.44 0.00 3.11
709 718 6.585416 AGCCAGATTGCCCAATTAATTAAAG 58.415 36.000 1.21 0.00 0.00 1.85
740 749 2.092598 AATGGCAGGATGGAAATCCC 57.907 50.000 1.07 0.00 41.65 3.85
743 752 3.017048 TCGAAATGGCAGGATGGAAAT 57.983 42.857 0.00 0.00 35.86 2.17
802 811 7.673810 AAACCGATTTAGAAAACGAAAAGTG 57.326 32.000 6.27 0.00 36.45 3.16
878 888 5.784578 TTTTTAGTTCCTTCTGGGCTTTC 57.215 39.130 0.00 0.00 34.39 2.62
948 959 2.806244 CCAAGGAAGAAAATGACGACGT 59.194 45.455 0.00 0.00 0.00 4.34
970 981 3.216371 TCCCCCTCCCCTGTTCCT 61.216 66.667 0.00 0.00 0.00 3.36
971 982 2.692741 CTCCCCCTCCCCTGTTCC 60.693 72.222 0.00 0.00 0.00 3.62
973 984 2.456840 CTCTCCCCCTCCCCTGTT 59.543 66.667 0.00 0.00 0.00 3.16
975 986 4.505970 CCCTCTCCCCCTCCCCTG 62.506 77.778 0.00 0.00 0.00 4.45
978 989 4.179599 CTCCCCTCTCCCCCTCCC 62.180 77.778 0.00 0.00 0.00 4.30
979 990 3.036959 TCTCCCCTCTCCCCCTCC 61.037 72.222 0.00 0.00 0.00 4.30
980 991 2.015726 TCTCTCCCCTCTCCCCCTC 61.016 68.421 0.00 0.00 0.00 4.30
981 992 2.018086 CTCTCTCCCCTCTCCCCCT 61.018 68.421 0.00 0.00 0.00 4.79
982 993 1.376249 ATCTCTCTCCCCTCTCCCCC 61.376 65.000 0.00 0.00 0.00 5.40
983 994 0.178935 CATCTCTCTCCCCTCTCCCC 60.179 65.000 0.00 0.00 0.00 4.81
984 995 0.178935 CCATCTCTCTCCCCTCTCCC 60.179 65.000 0.00 0.00 0.00 4.30
985 996 0.178935 CCCATCTCTCTCCCCTCTCC 60.179 65.000 0.00 0.00 0.00 3.71
986 997 0.178935 CCCCATCTCTCTCCCCTCTC 60.179 65.000 0.00 0.00 0.00 3.20
987 998 0.631998 TCCCCATCTCTCTCCCCTCT 60.632 60.000 0.00 0.00 0.00 3.69
988 999 0.266152 TTCCCCATCTCTCTCCCCTC 59.734 60.000 0.00 0.00 0.00 4.30
1192 1217 3.566742 TGATGGATTGATCGCAGGAAATG 59.433 43.478 0.00 0.00 0.00 2.32
1206 1231 4.592351 AGAGGATGAACGAGATGATGGATT 59.408 41.667 0.00 0.00 0.00 3.01
1217 1242 1.671328 CTGCGAGTAGAGGATGAACGA 59.329 52.381 0.00 0.00 0.00 3.85
1250 1275 2.769893 TCGGTAAAAGAAAACTCCGGG 58.230 47.619 0.00 0.00 38.70 5.73
1293 1318 6.307558 CCGATCGATCTTGATCAGTTGAATAG 59.692 42.308 22.43 1.44 44.02 1.73
1636 1674 2.678580 TGTGCTCGGATCGGGACA 60.679 61.111 0.00 1.75 0.00 4.02
1699 1737 2.106938 TAGCTGCCGCGATTGAGG 59.893 61.111 8.23 0.00 42.32 3.86
1908 1949 0.798776 CTAAACTTGCGTGCCTCCTG 59.201 55.000 0.00 0.00 0.00 3.86
1914 1955 1.463444 CACCTACCTAAACTTGCGTGC 59.537 52.381 0.00 0.00 0.00 5.34
2005 2046 4.222366 GGGACCGAGGGAGTAATTTATAGG 59.778 50.000 0.00 0.00 0.00 2.57
2023 2064 4.748600 GCTAGACGTTTACATTATGGGACC 59.251 45.833 0.00 0.00 0.00 4.46
2047 2088 7.021873 ACTCTCTCTGTCCCATAATCCATAAT 58.978 38.462 0.00 0.00 0.00 1.28
2048 2089 6.385443 ACTCTCTCTGTCCCATAATCCATAA 58.615 40.000 0.00 0.00 0.00 1.90
2049 2090 5.970289 ACTCTCTCTGTCCCATAATCCATA 58.030 41.667 0.00 0.00 0.00 2.74
2050 2091 4.825445 ACTCTCTCTGTCCCATAATCCAT 58.175 43.478 0.00 0.00 0.00 3.41
2051 2092 4.271807 ACTCTCTCTGTCCCATAATCCA 57.728 45.455 0.00 0.00 0.00 3.41
2052 2093 6.013379 TGATACTCTCTCTGTCCCATAATCC 58.987 44.000 0.00 0.00 0.00 3.01
2053 2094 6.945435 TCTGATACTCTCTCTGTCCCATAATC 59.055 42.308 0.00 0.00 0.00 1.75
2075 2116 9.809096 TTTACTGAAGATGCTCTTAGTTATCTG 57.191 33.333 0.00 0.00 36.73 2.90
2094 2135 6.039941 ACCGTCAAATTTGAACCATTTACTGA 59.960 34.615 22.07 0.00 39.21 3.41
2097 2138 5.631929 GGACCGTCAAATTTGAACCATTTAC 59.368 40.000 22.07 7.30 39.21 2.01
2100 2141 3.639094 TGGACCGTCAAATTTGAACCATT 59.361 39.130 22.07 5.70 39.21 3.16
2114 2155 3.139077 ACATCTTCAGTTTTGGACCGTC 58.861 45.455 0.00 0.00 0.00 4.79
2115 2156 3.208747 ACATCTTCAGTTTTGGACCGT 57.791 42.857 0.00 0.00 0.00 4.83
2127 2169 5.765677 TGACGGTCCAAATTTTACATCTTCA 59.234 36.000 5.55 0.00 0.00 3.02
2158 2200 4.674362 GCGTTTTTCGGAGCTCCAAAATAT 60.674 41.667 31.67 0.00 40.26 1.28
2159 2201 3.365565 GCGTTTTTCGGAGCTCCAAAATA 60.366 43.478 31.67 18.49 40.26 1.40
2185 2227 4.400251 TCAATTTGGATCATCTGTTGGAGC 59.600 41.667 0.00 0.00 0.00 4.70
2198 2240 5.337813 GCTCTTTTGGACCATCAATTTGGAT 60.338 40.000 3.10 0.00 39.25 3.41
2342 2385 8.404107 TGATTGAAACTATGATGATGATGCAT 57.596 30.769 0.00 0.00 0.00 3.96
2391 2437 4.998051 TGCTCTTTTGGTAGAGGGATTTT 58.002 39.130 0.00 0.00 41.60 1.82
2480 2526 2.203294 ACAAGGCCGGTGGTGTTC 60.203 61.111 13.32 0.00 0.00 3.18
2602 2649 0.107410 GGCAACATGACCGGTATGGA 60.107 55.000 7.34 0.00 42.00 3.41
2746 2817 2.559698 TTTGGCGGAAACATGAGAGA 57.440 45.000 0.00 0.00 0.00 3.10
2750 2821 3.810579 GCATTTGGCGGAAACATGA 57.189 47.368 0.00 0.00 0.00 3.07
2831 2902 1.228367 GGCATGGGAGGTGCTATGG 60.228 63.158 0.00 0.00 42.16 2.74
2832 2903 0.250640 GAGGCATGGGAGGTGCTATG 60.251 60.000 0.00 0.00 42.16 2.23
2833 2904 1.422161 GGAGGCATGGGAGGTGCTAT 61.422 60.000 0.00 0.00 42.16 2.97
2834 2905 2.072487 GGAGGCATGGGAGGTGCTA 61.072 63.158 0.00 0.00 42.16 3.49
2835 2906 3.415087 GGAGGCATGGGAGGTGCT 61.415 66.667 0.00 0.00 42.16 4.40
2836 2907 3.412624 GAGGAGGCATGGGAGGTGC 62.413 68.421 0.00 0.00 41.78 5.01
2837 2908 2.750657 GGAGGAGGCATGGGAGGTG 61.751 68.421 0.00 0.00 0.00 4.00
2838 2909 2.367512 GGAGGAGGCATGGGAGGT 60.368 66.667 0.00 0.00 0.00 3.85
2839 2910 3.174265 GGGAGGAGGCATGGGAGG 61.174 72.222 0.00 0.00 0.00 4.30
2840 2911 1.773391 ATGGGAGGAGGCATGGGAG 60.773 63.158 0.00 0.00 0.00 4.30
2841 2912 2.080536 CATGGGAGGAGGCATGGGA 61.081 63.158 0.00 0.00 0.00 4.37
2842 2913 2.519441 CATGGGAGGAGGCATGGG 59.481 66.667 0.00 0.00 0.00 4.00
2883 3014 8.831715 TGATTACATGTATGCGTCATAAGAAT 57.168 30.769 6.36 0.00 0.00 2.40
2884 3015 8.831715 ATGATTACATGTATGCGTCATAAGAA 57.168 30.769 6.36 0.00 35.21 2.52
2887 3018 8.776376 ATGATGATTACATGTATGCGTCATAA 57.224 30.769 26.01 17.92 36.82 1.90
2888 3019 8.776376 AATGATGATTACATGTATGCGTCATA 57.224 30.769 26.73 12.77 36.82 2.15
2889 3020 7.677454 AATGATGATTACATGTATGCGTCAT 57.323 32.000 23.83 23.83 36.82 3.06


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.